Bacterial and fungal infections have resulted in serious crop diseases, posing severe threats to food security. There is an urgent need to develop innovative antibacterial strategies to manage microbial infections. Herein, we fabricated a novel charge-switchable nanocomposite demonstrating pH-responsive infiltration into an acidic biofilm for heterocycles synergistic Zn²⁺ eradication of the Gram-negative bacteria (E. coli), Gram-positive bacteria (S. aureus) and fungi (R. Solani) biofilm with negligible harm to normal tissues. Originally, by stabilizing the Zn²⁺/heterocycles nanocomposite with the pH-sensitive functional carboxymethyl chitosan (DA-CMCS) via a facile aqueous one pot flash nanoprecipitation (FNP), the nanocomposite DA-CMCS@Zn²⁺@heterocycles was finely prepared. Due to the amide group of DA-CMCS was sensitive to pH variations and could be rapidly hydrolyzed, the DA-CMCS@Zn²⁺@heterocycles nanocomposite shows perfect surface charge change from negative charge at healthy pH (7.4) to positive charge at acidic biofilm pH (5.5). Thus, the nanocomposite with nano-scale size and positive charge are favorable for enhanced strong adherence to the negatively charged surfaces of microorganisms against plant disease. The present research contributes a prospective idea to the development of charge-switchable heterocycles/metal nanocomposites for effective inhibition microbial infections, showing a great potential of application in the modern agricultural industry.